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OPENSEQ.org

AraC GapRand FL2

ID: 1497642910 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 501 (501)
Sequences: 987 (987)
Seq/Len: 1.970
Nf(neff/√len): 44.1

HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 1.970).

Sequences per length for each position, AFTER the coverage/gap filter was applied
Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

Trim query Generate MSA using: Filter MSA GREMLIN
Start: End: E-value: Iterations: Coverage: Remove gaps: Prior:

GREMLIN Results:
Residue pairs sorted by coevolution strength:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

ij Scaled score Prob
213_H217_N1.7150.96
443_P447_R1.6650.95
265_H298_E1.6620.95
267_S271_G1.6130.94
275_N295_G1.5920.94
321_A337_N1.5780.93
275_N320_E1.5410.92
163_Q262_H1.5170.91
406_K411_T1.5140.91
345_Y349_H1.5110.91
217_N275_N1.5060.91
271_G302_S1.5020.91
275_N358_N1.4790.90
431_F435_F1.4750.90
262_H320_E1.4730.90
274_I395_S1.4670.90
114_A274_I1.4640.89
389_L393_V1.4410.88
262_H321_A1.4410.88
295_G302_S1.4370.88
94_A157_V1.4350.88
262_H267_S1.4320.88
271_G298_E1.4200.87
99_L108_F1.4140.87
267_S274_I1.4120.87
263_Q295_G1.4030.87
265_H275_N1.3980.86
429_L432_S1.3950.86
264_P298_E1.3690.85
150_T153_G1.3640.84
435_F443_P1.3620.84
275_N337_N1.3390.83
137_R140_G1.3390.83
377_S380_R1.3300.82
275_N298_E1.3240.82
220_S248_N1.3170.82
267_S298_E1.3160.81
108_F117_T1.3150.81
262_H275_N1.3110.81
320_E337_N1.3060.81
444_S447_R1.3040.81
163_Q275_N1.3040.81
220_S263_Q1.2980.80
263_Q271_G1.2960.80
158_K220_S1.2850.79
430_Y435_F1.2820.79
262_H337_N1.2820.79
135_I313_L1.2790.79
257_A274_I1.2790.79
151_I252_F1.2790.79
158_K167_E1.2740.78
445_E448_A1.2660.78
432_S442_S1.2630.78
122_N298_E1.2620.78
271_G295_G1.2600.77
134_F164_G1.2590.77
335_M426_D1.2520.77
442_S447_R1.2460.76
424_G435_F1.2450.76
424_G431_F1.2440.76
265_H426_D1.2380.76
121_A129_G1.2370.76
416_I446_F1.2370.76
99_L113_V1.2340.75
99_L117_T1.2300.75
453_K457_V1.2290.75
443_P446_F1.2280.75
248_N268_D1.2240.74
262_H358_N1.2220.74
441_A448_A1.2180.74
249_T252_F1.2160.74
103_G112_L1.2160.74
99_L118_P1.2130.74
399_D434_V1.2130.74
396_W400_Q1.2130.74
427_D430_Y1.2130.74
424_G430_Y1.2100.73
199_W206_F1.2080.73
163_Q265_H1.2080.73
267_S337_N1.2040.73
163_Q358_N1.2010.72
98_P108_F1.2010.72
432_S435_F1.2010.72
113_V118_P1.1990.72
391_I426_D1.1960.72
108_F115_G1.1960.72
163_Q298_E1.1940.72
429_L442_S1.1900.71
167_E220_S1.1890.71
108_F113_V1.1890.71
165_R262_H1.1890.71
150_T155_G1.1860.71
217_N264_P1.1860.71
199_W203_W1.1860.71
431_F443_P1.1840.71
115_G132_D1.1840.71
267_S275_N1.1810.71
117_T132_D1.1750.70
163_Q175_I1.1740.70
262_H274_I1.1740.70
302_S391_I1.1740.70
203_W206_F1.1680.69
188_R205_Y1.1670.69
137_R150_T1.1660.69
114_A122_N1.1610.69
442_S446_F1.1550.68
163_Q267_S1.1540.68
379_S383_H1.1530.68
122_N151_I1.1520.68
252_F271_G1.1500.68
220_S358_N1.1480.68
424_G443_P1.1480.68
167_E248_N1.1480.68
99_L132_D1.1470.67
114_A395_S1.1470.67
158_K165_R1.1450.67
265_H335_M1.1440.67
409_L424_G1.1420.67
110_A114_A1.1420.67
275_N321_A1.1420.67
201_H205_Y1.1420.67
119_I135_I1.1420.67
115_G119_I1.1400.67
98_P118_P1.1380.67
407_L417_A1.1370.66
108_F118_P1.1360.66
97_D104_Y1.1330.66
108_F132_D1.1330.66
380_R385_F1.1310.66
95_Q100_L1.1310.66
197_R265_H1.1290.66
122_N275_N1.1270.65
112_L115_G1.1250.65
435_F447_R1.1250.65
335_M391_I1.1200.65
439_T448_A1.1190.65
113_V117_T1.1190.65
293_G333_P1.1180.65
374_V378_P1.1180.65
430_Y443_P1.1170.64
102_P108_F1.1170.64
428_Q444_S1.1130.64
168_F179_P1.1130.64
439_T446_F1.1120.64
427_D432_S1.1110.64
373_H378_P1.1100.64
435_F440_G1.1080.64
264_P268_D1.1070.63
97_D111_H1.1060.63
177_L180_P1.1050.63
186_Y199_W1.1040.63
440_G443_P1.1040.63
380_R383_H1.1020.63
172_P266_F1.1020.63
342_A364_V1.1000.63
141_M144_G1.0990.63
264_P426_D1.0980.62
430_Y447_R1.0950.62
195_E248_N1.0950.62
113_V119_I1.0950.62
377_S385_F1.0950.62
132_D144_G1.0940.62
250_G303_E1.0930.62
99_L104_Y1.0920.62
137_R153_G1.0920.62
302_S335_M1.0900.62
298_E335_M1.0880.61
263_Q267_S1.0870.61
412_T423_V1.0830.61
430_Y442_S1.0830.61
107_S228_A1.0820.61
388_Q417_A1.0820.61
104_Y108_F1.0820.61
165_R220_S1.0810.61
154_Q157_V1.0800.61
323_N333_P1.0790.60
411_T420_G1.0790.60
432_S443_P1.0780.60
175_I426_D1.0780.60
102_P117_T1.0770.60
98_P113_V1.0750.60
122_N264_P1.0740.60
376_L380_R1.0740.60
98_P117_T1.0730.60
272_Q298_E1.0720.60
267_S320_E1.0710.60
115_G118_P1.0690.59
342_A399_D1.0660.59
436_K439_T1.0640.59
267_S395_S1.0640.59
99_L115_G1.0630.59
222_F228_A1.0620.59
130_Y189_H1.0620.59
115_G131_L1.0610.59
404_Q410_S1.0570.58
199_W208_P1.0560.58
397_R400_Q1.0550.58
163_Q320_E1.0530.58
377_S383_H1.0530.58
98_P104_Y1.0510.57
379_S385_F1.0510.57
114_A117_T1.0490.57
167_E341_E1.0490.57
98_P115_G1.0490.57
417_A428_Q1.0470.57
305_L308_N1.0470.57
222_F387_Q1.0470.57
180_P186_Y1.0470.57
432_S447_R1.0460.57
170_C294_Q1.0460.57
271_G293_G1.0450.57
271_G332_H1.0440.57
407_L428_Q1.0430.57
163_Q220_S1.0420.56
348_D359_F1.0410.56
203_W208_P1.0400.56
112_L119_I1.0390.56
386_R399_D1.0390.56
333_P415_P1.0390.56
208_P212_W1.0380.56
302_S332_H1.0380.56
131_L141_M1.0370.56
94_A313_L1.0370.56
168_F176_L1.0360.56
293_G306_A1.0340.56
310_L314_L1.0330.55
386_R434_V1.0320.55
254_P399_D1.0320.55
217_N262_H1.0310.55
273_I309_L1.0310.55
424_G440_G1.0300.55
380_R384_L1.0300.55
95_Q103_G1.0300.55
268_D293_G1.0300.55
438_C448_A1.0260.55
144_G148_N1.0260.55
134_F151_I1.0260.55
267_S321_A1.0240.55
364_V373_H1.0230.54
179_P263_Q1.0230.54
147_L151_I1.0210.54
323_N337_N1.0210.54
99_L109_N1.0200.54
378_P384_L1.0180.54
154_Q171_R1.0170.54
309_L313_L1.0140.53
200_Y211_Y1.0140.53
197_R220_S1.0140.53
431_F447_R1.0130.53
179_P182_E1.0130.53
99_L102_P1.0120.53
93_E116_L1.0120.53
95_Q102_P1.0110.53
199_W212_W1.0100.53
183_I222_F1.0100.53
113_V131_L1.0100.53
108_F112_L1.0090.53
132_D140_G1.0090.53
98_P112_L1.0070.53
212_W218_W1.0070.53
438_C441_A1.0070.53
264_P335_M1.0070.53
410_S438_C1.0060.53
151_I391_I1.0060.53
98_P119_I1.0050.52
95_Q104_Y1.0050.52
104_Y118_P1.0050.52
429_L433_R1.0050.52
134_F295_G1.0050.52
118_P132_D1.0040.52
122_N130_Y1.0030.52
110_A118_P1.0020.52
155_G173_G1.0000.52
293_G319_M1.0000.52
348_D414_M1.0000.52
Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
NEW Features
HHsearch Results: (06Aug15)
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
PDB M Cov P(%) HHΔ  
3gbgA10.51799.90.751Contact Map
2k9sA10.213699.80.797Contact Map
3oioA10.223699.80.802Contact Map
3oouA10.209699.80.803Contact Map
3mn2A20.211699.80.803Contact Map
1bl0A10.231599.80.803Contact Map
3w6vA10.221699.80.809Contact Map
3mklA20.221699.80.813Contact Map
3lsgA50.205699.80.814Contact Map
1d5yA40.311499.70.82Contact Map
M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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